Table of Contents

Chapter 1: Considerations for Lipid Force Field DevelopmentJeffery B. Klauda, Richard M. Venable, Alexander D. MacKerell, Jr. , and Richard W. PastorChapter 2: Electrostatics in Biomolecular Simulations: Where Are We Now and Where We Are HeadedMikko Karttunen, Jorg Rottler, Ilpo Vattulainen, and Celeste SaguiChapter 3: Time and Length Scales in Lipid Bilayer SimulationsOlle Edholm Chapter 4: Molecular dynamics simulation of lipid-protein interactionsNicolas Sapay and D. Peter TielemanChapter 5: Implicit Modeling of MembranesAlan GrossfieldChapter 6: Blue Matter: Scaling of N-Body Simulations to One Atom per Node Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, T.J. Christopher Ward, Mark Giampapa, Michael C. Pitman, Jed Pitera, William C. Swope, and Robert S. GermainChapter 7: Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic BehaviorGary S. Ayton, Sergei Izvekov, W. G. Noid , and Gregory A. VothChapter 8: Small Molecule Interactions with Lipid BilayersPeter Tieleman and Justin MacCollumChapter 9: On the nature of lipid rafts: Insights from molecularly detailed simulations of model biological membranes containing mixtures of cholesterol and phospholipidsMax Berkowitz Chapter 10: Atomistic and Mean Field Simulations of Lateral Organization in MembranesSagar A Pandit, See-wing Chiu, Eric Jakobsson, and Larry ScottChapter 11: Molecular modeling of the structural properties and formation of high-density lipoprotein particlesAmy Y. Shih, Peter L. Freddolino, Anton Arkhipov, Stephen G. Sligar, and Klaus SchultenChapter 12: Gas Conduction of Lipid Bilayers and Membrane ChannelsYi Wang, Y. Zenmei Ohkubo and Emad Tajkhorshid Chapter 13: An introduction to voltage-gated K+ channelsBenoit Roux Chapter 14: Computational Models for Electrified InterfacesElizabeth J Denning and Thomas B WoolfChapter 15: Charged protein side chain movement in lipid bilayers explored with free energy simulation Libo Li, Igor Vorobyov, Sudha Dorairaj and Toby W. Allen